Comparison of nearest neighbor analysis for tiling arrays and RNA-Seq. (a) Correlation of TARs using intensities determined by RNA-Seq and tiling array. The colors scheme is identical to that in Figure 6a. As expected due to cross-hybridization, TARs with high similarity scores are called expressed by tiling arrays but not by RNA-Seq. (b) Density plot showing fraction of TARs (y-axis) with a given RNA-Seq expression level (x-axis). As above, TARs are segregated by similarity. It is clear that TARs with the highest similarity (red) fall in a different distribution and are generally not expressed according to the RNA-Seq data. (c) Similar but x-axis is the TAR intensity from tiling arrays. In this case, highly similar TARs are more likely to be highly expressed, suggestive of cross-hybridization. The distribution of highly similar TARs exhibits a bump, possibly due to more highly expressed TARs being more likely to exhibit cross-hybridization.